FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles

Sergei Põlme; Kessy Abarenkov; R. Henrik Nilsson; Björn D. Lindahl; Karina Engelbrecht Clemmensen; Havard Kauserud; Nhu Nguyen; Rasmus Kjøller; Scott T. Bates; Petr Baldrian; Tobias Guldberg Frøslev; Kristjan Adojaan; Alfredo Vizzini; Ave Suija; Donald Pfister; Hans Otto Baral; Helle Järv; Hugo Madrid; Jenni Nordén; Jian Kui Liu; Julia Pawlowska; Kadri Põldmaa; Kadri Pärtel; Kadri Runnel; Karen Hansen; Karl Henrik Larsson; Kevin David Hyde; Marcelo Sandoval-Denis; Matthew E. Smith; Merje Toome-Heller; Nalin N. Wijayawardene; Nelson Menolli; Nicole K. Reynolds; Rein Drenkhan; Sajeewa S.N. Maharachchikumbura; Tatiana B. Gibertoni; Thomas Læssøe; William Davis; Yuri Tokarev; Adriana Corrales; Adriene Mayra Soares; Ahto Agan; Alexandre Reis Machado; Andrés Argüelles-Moyao; Andrew Detheridge; Angelina de Meiras-Ottoni; Annemieke Verbeken; Arun Kumar Dutta; Bao Kai Cui; C. K. Pradeep

doi:10.1007/s13225-020-00466-2

FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles

Título traducido de la contribución: FungalTraits: una base de datos de rasgos fácil de usar de hongos y stramenopiles similares a hongos

, Sergei Põlme, Kessy Abarenkov, R. Henrik Nilsson, Björn D. Lindahl, Karina Engelbrecht Clemmensen, Havard Kauserud, Nhu Nguyen, Rasmus Kjøller, Scott T. Bates, Petr Baldrian, Tobias Guldberg Frøslev, Kristjan Adojaan, Alfredo Vizzini, Ave Suija, Donald Pfister, Hans Otto Baral, Helle Järv, Hugo Madrid, Jenni NordénJian Kui Liu, Julia Pawlowska, Kadri Põldmaa, Kadri Pärtel, Kadri Runnel, Karen Hansen, Karl Henrik Larsson, Kevin David Hyde, Marcelo Sandoval-Denis, Matthew E. Smith, Merje Toome-Heller, Nalin N. Wijayawardene, Nelson Menolli, Nicole K. Reynolds, Rein Drenkhan, Sajeewa S.N. Maharachchikumbura, Tatiana B. Gibertoni, Thomas Læssøe, William Davis, Yuri Tokarev, Adriana Corrales, Adriene Mayra Soares, Ahto Agan, Alexandre Reis Machado, Andrés Argüelles-Moyao, Andrew Detheridge, Angelina de Meiras-Ottoni, Annemieke Verbeken, Arun Kumar Dutta, Bao Kai Cui, C. K. Pradeep

Producción científica: Contribución a una revista › Artículo de Investigación › revisión exhaustiva

531 Citas (Scopus)

Resumen

El estilo de vida críptico de la mayoría de los hongos requiere la identificación molecular del gremio en estudios ambientales. Durante las últimas décadas, el rápido desarrollo y la asequibilidad de las herramientas moleculares han mejorado enormemente la comprensión de la diversidad de hongos en todos los ecosistemas y hábitats. Sin embargo, a pesar del progreso de los métodos moleculares, el conocimiento sobre las propiedades funcionales de los taxones de hongos es vago y la interpretación de los estudios ambientales de una manera ecológicamente significativa sigue siendo un desafío. Con el fin de facilitar las asignaciones funcionales y la interpretación ecológica de los estudios ambientales, presentamos una base de datos de características y caracteres de fácil uso FungalTraits que operan a nivel de hipótesis de género y especie. Combinando la información de esfuerzos anteriores como FUNGuild y FunFun junto con la participación del conocimiento experto, volvimos a anotar 10,210 y 151 géneros de hongos y Stramenopila, respectivamente. Esto resultó en un conjunto de datos de hoja de cálculo independiente que cubre 17 rasgos relacionados con el estilo de vida de los géneros de hongos y Stramenopila, diseñado para asignaciones funcionales rápidas de estudios ambientales. Para asignar los estados de rasgo a las hipótesis de especies de hongos, la comunidad científica de expertos categorizó y asignó manualmente la información de rasgo disponible a 697.413 secuencias de ITS de hongos. Sobre la base de esas secuencias, pudimos resumir la información del rasgo y del huésped en 92.623 hipótesis de especies de hongos con un umbral de disimilitud del 1%.

Título traducido de la contribución	FungalTraits: una base de datos de rasgos fácil de usar de hongos y stramenopiles similares a hongos
Idioma original	Inglés estadounidense
Páginas (desde-hasta)	1-16
Número de páginas	16
Publicación	Fungal Diversity
Volumen	105
N.º	1
DOI	https://doi.org/10.1007/s13225-020-00466-2
Estado	Publicada - nov. 2020

Áreas temáticas de ASJC Scopus

Ecología, evolución, comportamiento y sistemática
Ecología

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, Põlme, S., Abarenkov, K., Henrik Nilsson, R., Lindahl, B. D., Clemmensen, K. E., Kauserud, H., Nguyen, N., Kjøller, R., Bates, S. T., Baldrian, P., Frøslev, T. G., Adojaan, K., Vizzini, A., Suija, A., Pfister, D., Baral, H. O., Järv, H., Madrid, H., ... Pradeep, C. K. (2020). FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity, 105(1), 1-16. https://doi.org/10.1007/s13225-020-00466-2

@article{9267826021fe40b8b35ec13c20cb69e6,

title = "FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles",

abstract = "The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.",

author = "Sergei P{\~o}lme and Kessy Abarenkov and {Henrik Nilsson}, R. and Lindahl, {Bj{\"o}rn D.} and Clemmensen, {Karina Engelbrecht} and Havard Kauserud and Nhu Nguyen and Rasmus Kj{\o}ller and Bates, {Scott T.} and Petr Baldrian and Fr{\o}slev, {Tobias Guldberg} and Kristjan Adojaan and Alfredo Vizzini and Ave Suija and Donald Pfister and Baral, {Hans Otto} and Helle J{\"a}rv and Hugo Madrid and Jenni Nord{\'e}n and Liu, {Jian Kui} and Julia Pawlowska and Kadri P{\~o}ldmaa and Kadri P{\"a}rtel and Kadri Runnel and Karen Hansen and Larsson, {Karl Henrik} and Hyde, {Kevin David} and Marcelo Sandoval-Denis and Smith, {Matthew E.} and Merje Toome-Heller and Wijayawardene, {Nalin N.} and Nelson Menolli and Reynolds, {Nicole K.} and Rein Drenkhan and Maharachchikumbura, {Sajeewa S.N.} and Gibertoni, {Tatiana B.} and Thomas L{\ae}ss{\o}e and William Davis and Yuri Tokarev and Adriana Corrales and Soares, {Adriene Mayra} and Ahto Agan and Machado, {Alexandre Reis} and Andr{\'e}s Arg{\"u}elles-Moyao and Andrew Detheridge and {de Meiras-Ottoni}, Angelina and Annemieke Verbeken and Dutta, {Arun Kumar} and Cui, {Bao Kai} and Pradeep, {C. K.}",

note = "Funding Information: We thank Dr. Mario Saare for help with the R software. Publisher Copyright: {\textcopyright} 2021, MUSHROOM RESEARCH FOUNDATION. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

year = "2020",

month = nov,

doi = "10.1007/s13225-020-00466-2",

language = "English (US)",

volume = "105",

pages = "1--16",

journal = "Fungal Diversity",

issn = "1560-2745",

publisher = "Springer Netherlands",

number = "1",

}

Põlme, S, Abarenkov, K, Henrik Nilsson, R, Lindahl, BD, Clemmensen, KE, Kauserud, H, Nguyen, N, Kjøller, R, Bates, ST, Baldrian, P, Frøslev, TG, Adojaan, K, Vizzini, A, Suija, A, Pfister, D, Baral, HO, Järv, H, Madrid, H, Nordén, J, Liu, JK, Pawlowska, J, Põldmaa, K, Pärtel, K, Runnel, K, Hansen, K, Larsson, KH, Hyde, KD, Sandoval-Denis, M, Smith, ME, Toome-Heller, M, Wijayawardene, NN, Menolli, N, Reynolds, NK, Drenkhan, R, Maharachchikumbura, SSN, Gibertoni, TB, Læssøe, T, Davis, W, Tokarev, Y, Corrales, A, Soares, AM, Agan, A, Machado, AR, Argüelles-Moyao, A, Detheridge, A, de Meiras-Ottoni, A, Verbeken, A, Dutta, AK & Cui, BK & Pradeep, CK 2020, 'FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles', Fungal Diversity, vol. 105, n.º 1, pp. 1-16. https://doi.org/10.1007/s13225-020-00466-2

TY - JOUR

T1 - FungalTraits

T2 - a user-friendly traits database of fungi and fungus-like stramenopiles

AU - Põlme, Sergei

AU - Abarenkov, Kessy

AU - Henrik Nilsson, R.

AU - Lindahl, Björn D.

AU - Clemmensen, Karina Engelbrecht

AU - Kauserud, Havard

AU - Nguyen, Nhu

AU - Kjøller, Rasmus

AU - Bates, Scott T.

AU - Baldrian, Petr

AU - Frøslev, Tobias Guldberg

AU - Adojaan, Kristjan

AU - Vizzini, Alfredo

AU - Suija, Ave

AU - Pfister, Donald

AU - Baral, Hans Otto

AU - Järv, Helle

AU - Madrid, Hugo

AU - Nordén, Jenni

AU - Liu, Jian Kui

AU - Pawlowska, Julia

AU - Põldmaa, Kadri

AU - Pärtel, Kadri

AU - Runnel, Kadri

AU - Hansen, Karen

AU - Larsson, Karl Henrik

AU - Hyde, Kevin David

AU - Sandoval-Denis, Marcelo

AU - Smith, Matthew E.

AU - Toome-Heller, Merje

AU - Wijayawardene, Nalin N.

AU - Menolli, Nelson

AU - Reynolds, Nicole K.

AU - Drenkhan, Rein

AU - Maharachchikumbura, Sajeewa S.N.

AU - Gibertoni, Tatiana B.

AU - Læssøe, Thomas

AU - Davis, William

AU - Tokarev, Yuri

AU - Corrales, Adriana

AU - Soares, Adriene Mayra

AU - Agan, Ahto

AU - Machado, Alexandre Reis

AU - Argüelles-Moyao, Andrés

AU - Detheridge, Andrew

AU - de Meiras-Ottoni, Angelina

AU - Verbeken, Annemieke

AU - Dutta, Arun Kumar

AU - Cui, Bao Kai

AU - Pradeep, C. K.

N1 - Funding Information: We thank Dr. Mario Saare for help with the R software. Publisher Copyright: © 2021, MUSHROOM RESEARCH FOUNDATION. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2020/11

Y1 - 2020/11

N2 - The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.

AB - The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.

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DO - 10.1007/s13225-020-00466-2

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FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles

Resumen

Áreas temáticas de ASJC Scopus

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Huella

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